JADOPPT: java based AutoDock preparing and processing tool

[EN]Motivation: AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results. Availability and Implementation: JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http://visualanalytics.land/cgarcia/JADOPPT.html Contacts: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization

Probing for Instanton Quarks with epsilon-Cooling

We use epsilon-cooling, adjusting at will the order a^2 corrections to the lattice action, to study the parameter space of instantons in the background of non-trivial holonomy and to determine the presence and nature of constituents with fractional topological charge at finite and zero temperature for SU(2). As an additional tool, zero temperature configurations were generated from those at finite temperature with well-separated constituents. This is achieved by "adiabatically" adjusting the anisotropic coupling used to implement finite temperature on a symmetric lattice. The action and topological charge density, as well as the Polyakov loop and chiral zero-modes are used to analyse these configurations. We also show how cooling histories themselves can reveal the presence of constituents with fractional topological charge. We comment on the interpretation of recent fermion zero-mode studies for thermalized ensembles at small temperatures.Comment: 26 pages, 14 figures in 33 part

Mitochondrial DNA genetic relationships at the ancient Neolithic site of Tell Halula

The extent of racemization of aspartic acid (Asp) -expressed as D/L ratio- has been used as a marker of biomolecular degradation in ancient remains. However, Asp racemization rate is highly variable, and depends on biochemical and geochemical factors. In this paper we aim to determine to which extent the fraction analyzed and the kind of sample used may influence the D/L Asp ratios. Other factors, such as burial site and sample preservation conditions, are also considered. D/L Asp ratios were obtained in 38 ancient human samples from 30 different individuals in which Real Time PCR quantification and amplification of short mtDNA fragments had been previously achieved. Four samples were taken from bones, 16 from whole teeth and 18 from dentine. In 7 cases whole tooth and dentine fractions from the same individual were analyzed. The samples belonged to 8 archaeological sites from Pre-pottery Neolithic B (PPNB), Cardial Neolithic and Chalcolithic time periods. Results show significant differences between the D/L Asp ratios obtained in dentine and whole tooth fractions from the same tooth and individual, as well as among dentine samples from the same archaeological site and among samples of the same age from different, though nearby, archaeological sites. Ancient DNA (aDNA) could be characterized in the majority of the samples, independently from their racemization values, which suggests that other factors, apart from the sample preservation stage, are more significantly affecting the racemization rate. A generalized use of the Asp racemization ratio as a threshold value for ancient DNA preservation needs to be questioned until further methodological standardization is considered

Editorial

[EN] Para este número 5 de la revista de investigación en artes visuales ANIAV, hemos seleccionado diez trabajos de indudable calidad e interés. Estos trabajos fueron recomendados por los revisores de entre los casi doscientos trabajos sometidos al sistema de doble ciego para el IV Congreso Internacional de Investigación en Artes Visuales ANIAV 2019. IMAGEN [N] VISIBLE. Se invitó a los autores seleccionados a revisar sus trabajos adecuándolas a las normas de la revista y a presentarlos en la plataforma para una nueva revisión por pares ciegos. De estos trabajos seleccionados se publicó solo un resumen en las actas del congreso y es en exclusivamente en este número 5, donde figuran corregidos y completos.Pérez García, E.; Martínez Arroyo, EJ.; Silva Dos Santos, FC. (2019). Editorial. ANIAV - Revista de Investigación en Artes Visuales. (5):V-VI. https://doi.org/10.4995/aniav.2019.12392SWORDVVI

Revista de Vertebrados de la Estación Biológica de Doñana

Datos sobre la fauna de anfibios del Bajo GuadalquivirDiet of the Black Vulture (Aegypius monachus) in the Iberian PeninsulaBiología de reproducción de una pareja de Hieraetus fasciatus en España central.Sobre la migraclon de la focha común (Fulica atra) en el Mediterráneo Occidental en base a la información de la Estación Biológica de laTour du Valat (Camargue, Francia)Problemática y medidas de conservación de la Foca fraile (Monachus monachus, Hermann 1779) en el Sahara OccidentaNuevas citas de sifonápteros parásitos de mamíferos en España.Contribución al estudio de Lacerta monticola en la Sierra de Gredos (Avila. España)A melanistic Spanish smooth snake (Coranella a. austriaca)Nueva localidad para Vipera b. berus en el. Norte de EspañaSegunda cita en España de Porphyrula alleni (Thomson, 1842)Peer reviewe

SATISFACCIÓN DE LOS ALUMNOS DE ENFERMERÍA DE LA UNIVERSIDAD CATÓLICA SAN ANTONIO (UCAM) SOBRE SU FORMACIÓN PRÁCTICA. SEMINARIOS EN SALAS DE DEMOSTRACIONES Y PRÁCTICAS CLÍNICAS

Objective: To know the satisfaction of UCAM nursing students regarding the clinical training included in the practical training they attended during the undergraduate program. Method: A descriptive, observational and transversal study was carried out with nursing students of the Catholic University of San Antonio during the academic years 2004/05 and 2007/08. The studied sample consisted of all the nursing students registered in courses of second and third year with clinical training credits. A closed specific questionnaire of multiple choice was elaborated for the accomplishment of the study. Results:  More than 90% of the students state that seminars improve the clinical training and that the theoretical study of practice seminars is helpful for improving nursing techniques. Techniques learned at seminars meet real assistance. Students of both academic years describe the relation with nurses and clinical mentors at hospitals and health centers as good and very good in more than 90% of the cases. More than 80% of the students consider that clinical mentors have facilitated its integration in working team. Conclusions: It is important that the student satisfaction in internal and external practice training is good and that the relation with clinical mentors is adequate. Regarding the opinion of the students about the clinical mentor management in the Unit of Nursing Practical Training, it was concluded that there are aspects to be improved in which we have already begun to work.Objetivo. Conocer la satisfacción de los alumnos de enfermería de la Universidad Católica San Antonio sobre las prácticas que desarrollan durante su formación de pregrado. Método. Se realizó un estudio descriptivo observacional trasversal realizado en la Diplomatura de Enfermería de la Universidad Católica San Antonio durante los cursos académicos 2004/05 y 2007/08. La población objeto de estudio son todos los alumnos de enfermería matriculados en asignaturas de segundo y tercer curso con créditos prácticos. Para la realización del estudio se elaboró un cuestionario específico cerrado de respuesta múltiple. Resultados. Más del 90% de los alumnos afirman que los seminarios mejoran el inicio de las prácticas clínicas, y que el estudio teórico de los seminarios prácticos es de gran ayuda para mejorar la técnica. Las técnicas aprendidas en los seminarios se corresponden con la realidad asistencial. Los alumnos de ambos cursos académicos califican la relación con los profesionales de los centros sanitarios y socio-sanitarios como buena y muy buena en más de un 90% de los casos. Más del 80% de los alumnos consideran que el profesional – tutor ha facilitado su integración en el equipo de trabajo. Conclusiones. Se puede subrayar que la satisfacción de los alumnos tanto en las prácticas internas y externas es buena y que la relación con los profesionales – tutores es adecuada. En cuanto a la opinión de los alumnos sobre las gestiones que se llevan a cabo desde la Unidad de Prácticas de Enfermería, concluimos que existen aspectos mejorables sobre los que ya hemos comenzado a trabajar.

Extremely Long-Lived Stigmas Allow Extended Cross-Pollination Opportunities in a High Andean Plant

High-elevation ecosystems are traditionally viewed as environments in which predominantly autogamous breeding systems should be selected because of the limited pollinator availability. Chaetanthera renifolia (Asteraceae) is an endemic monocarpic triennial herb restricted to a narrow altitudinal range within the high Andes of central Chile (3300–3500 m a.s.l.), just below the vegetation limit. This species displays one of the larger capitulum within the genus. Under the reproductive assurance hypothesis, and considering its short longevity (monocarpic triennial), an autogamous breeding system and low levels of pollen limitation would be predicted for C. renifolia. In contrast, considering its large floral size, a xenogamous breeding system, and significant levels of pollen limitation could be expected. In addition, the increased pollination probability hypothesis predicts prolonged stigma longevity for high alpine plants. We tested these alternative predictions by performing experimental crossings in the field to establish the breeding system and to measure the magnitude of pollen limitation in two populations of C. renifolia. In addition, we measured the stigma longevity in unpollinated and open pollinated capitula, and pollinator visitation rates in the field. We found low levels of self-compatibility and significant levels of pollen limitation in C. renifolia. Pollinator visitation rates were moderate (0.047–0.079 visits per capitulum per 30 min). Although pollinator visitation rate significantly differed between populations, they were not translated into differences in achene output. Finally, C. renifolia stigma longevity of unpollinated plants was extremely long and significantly higher than that of open pollinated plants (26.3±2.8 days vs. 10.1±2.2, respectively), which gives support to the increased pollination probability hypothesis for high-elevation flowering plants. Our results add to a growing number of studies that show that xenogamous breeding systems and mechanisms to increase pollination opportunities can be selected in high-elevation ecosystems